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Background & Aims Noroviruses (NoVs) are the leading cause of acute gastroenteritis worldwide and are associated with significant morbidity and mortality. Moreover, an asymptomatic carrier state can persist following acute infection, promoting NoV spread and evolution. Thus, defining immune correlates of NoV protection and persistence is needed to guide the development of future vaccines and limit viral spread. Whereas antibody responses following NoV infection or vaccination have been studied extensively, cellular immunity has received less attention. Data from the mouse NoV model suggest that T cells are critical for preventing persistence and achieving viral clearance, but little is known about NoV-specific T-cell immunity in humans, particularly at mucosal sites. Methods We screened peripheral blood mononuclear cells from 3 volunteers with an overlapping NoV peptide library. We then used HLA-peptide tetramers to track virus-specific CD8+ T cells in peripheral, lymphoid, and intestinal tissues. Tetramer+ cells were further characterized using markers for cellular trafficking, exhaustion, cytotoxicity, and proliferation. Results We defined 7 HLA-restricted immunodominant class I epitopes that were highly conserved across pandemic strains from genogroup II.4. NoV-specific CD8+ T cells with central, effector, or tissue-resident memory phenotypes were present at all sites and were especially abundant in the intestinal lamina propria. The properties and differentiation states of tetramer+ cells varied across donors and epitopes. Conclusions Our findings are an important step toward defining the breadth, distribution, and properties of human NoV T-cell immunity. Moreover, the molecular tools we have developed can be used to evaluate future vaccines and engineer novel cellular therapeutics., Graphical abstract

Receptor Interacting Protein Kinases (RIPKs) are cellular signaling molecules that are critical for homeostatic signaling in both communicable and non-communicable disease processes. In particular, RIPK1, RIPK2, RIPK3 and RIPK7 have emerged as key mediators of intracellular signal transduction including inflammation, autophagy and programmed cell death, and are thus essential for the early control of many diverse pathogenic organisms. In this review, we discuss the role of each RIPK in host responses to bacterial and viral pathogens, with a focus on studies that have used pathogen infection models rather than artificial stimulation with purified pathogen associated molecular patterns. We also discuss the intricate mechanisms of host evasion by pathogens that specifically target RIPKs for inactivation, and finally, we will touch on the controversial issue of drug development for kinase inhibitors to treat chronic inflammatory and neurological disorders, and the implications this may have on the outcome of pathogen infections.

This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review., Graphical abstract Unlabelled Image, Highlights • An overview on virus occurrence, detection and viability in wastewater and sludge • Molecular methods are extensively used to detect viruses in wastewater. • Use of sequencing to monitor virus abundance and diversity in wastewater and sludge • Detection and quantification of viruses in wastewater to monitor disease outbreaks • Research need: studies on detection methods of emerging viruses such as SARS-CoV-2

Highlights • Dose-response model for pathogen infection developed on basis of thermodynamic association constants. • Fraction of pathogen oral dose surviving mucus barrier to reach intestinal epithelium modelled. • Fraction of host intestinal epithelial cells with bound pathogen modelled as function of dose. • Theory of parameterising thermodynamic association constants from molecular data developed. • Thermodynamics provides link between sequencing data and risk of infection., Assessing the risk of infection from emerging viruses or of existing viruses jumping the species barrier into novel hosts is limited by the lack of dose response data. The initial stages of the infection of a host by a virus involve a series of specific contact interactions between molecules in the host and on the virus surface. The strength of the interaction is quantified in the literature by the dissociation constant (Kd) which is determined experimentally and is specific for a given virus molecule/host molecule combination. Here, two stages of the initial infection process of host intestinal cells are modelled, namely escape of the virus in the oral challenge dose from the innate host defenses (e.g. mucin proteins in mucus) and the subsequent binding of any surviving virus to receptor molecules on the surface of the host epithelial cells. The strength of virus binding to host cells and to mucins may be quantified by the association constants, Ka and Kmucin, respectively. Here, a mechanistic dose-response model for the probability of infection of a host by a given virus dose is constructed using Ka and Kmucin which may be derived from published Kd values taking into account the number of specific molecular interactions. It is shown that the effectiveness of the mucus barrier is determined not only by the amount of mucin but also by the magnitude of Kmucin. At very high Kmucin values, slight excesses of mucin over virus are sufficient to remove all the virus according to the model. At lower Kmucin values, high numbers of virus may escape even with large excesses of mucin. The output from the mechanistic model is the probability (p1) of infection by a single virion which is the parameter used in conventional dose-response models to predict the risk of infection of the host from the ingested dose. It is shown here how differences in Ka (due to molecular differences in an emerging virus strain or new host) affect p1, and how these differences in Ka may be quantified in terms of two thermodynamic parameters, namely enthalpy and entropy. This provides the theoretical link between sequencing data and risk of infection. Lack of data on entropy is a limitation at present and may also affect our interpretation of Kd in terms of infectivity. It is concluded that thermodynamic approaches have a major contribution to make in developing dose-response models for emerging viruses.

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Objectives To investigate an outbreak of necrotizing enterocolitis (NEC) in a neonatal intensive care unit (NICU) and to identify the etiology, describe illness risk factors, and develop control measures. Study design A retrospective case-control study was performed including newborns with NEC and newborns without NEC, examining demographic factors and exposures to medications, staff members, and procedures before illness. Stool samples from affected newborns were collected and tested for bacteria, parasites, and viruses. Results We confirmed a NEC outbreak in the NICU in January 1998 with 8 cases, including 2 deaths, clustered in time and space. Norovirus-like particles were identified in all available stools from cases; norovirus (NoV) was confirmed with reverse transcriptase polymerase chain reaction in 4 of 6 samples. NEC cases were younger, had lower Apgar scores, and received antibiotics longer than 25 control subjects. Three NICU health care personnel had more contact with cases than control subjects; 1 staff member recalled having gastroenteritis symptoms around the time of the outbreak. Conclusions This report associates NoV with NEC. NoV appeared to precipitate NEC in predisposed infants. Spatial clustering and epidemiologic links between cases and a health care worker with gastroenteritis suggests that NoV should be investigated among the etiologies of NEC outbreaks and that interventions targeted to interruption of NoV transmission should be considered.